AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons015_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244706
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH384	249	unknown
#1	MTH387	24	conserved protein
#2	MTH388	35	unknown
#3	MTH393	41	NADH dehydrogenase (ubiquinone), subunit 1 related protein
#4	MTH394	55	unknown
#5	MTH746	96	endonuclease III related protein (probably non-iron-sulfur homolog)
#6	MTH1246	30	NADH dehydrogenase I, subunit N 
#7	MTH1251	147	conserved protein
#8	MTH1826	159	unknown (contains ferredoxin domain)

Motif 1
GGTTTCTGTGAATATAATCACGAAAACGACTATGA	0	62	1
CTCTACAGAAGATTTAGTAATAAATTTTAAGGATT	0	98	0
GGACCCTTCAGATATCAGTAAAAAAAAGTTTCTGT	0	133	1
GAAACCTCCAGATATTAGTAAAAAAGGCCATAATT	0	171	1
ACCTAAAAAAGACCTCTTAATAAAATTATGGCCTT	0	194	0
     ATATAAATCTTTTTAAAAAAGGTGAGTTAG	0	229	0
   AAGACATGATGTGGAATGAAAATGGAAGGGAT	4	7	1
AAATGGAAGGGATTTAATCAGAAAAGAGGGGATTT	4	29	1
ATACCCCGATGATATATTAATTAAAAGTTACACAG	5	17	0
TAAAATAGGGGATCCGATGATTAAACACTTGAAGG	7	43	0
ATTTTATTACGATTTATATAGAAAACTTTATATTA	7	72	1
CCCCCCTGAAGATCCTCTCAGAACACTTCAAAGAA	8	74	0
TCCTGTAAAAGATATCCTCAGAACAGAATATATAA	8	124	0
          *** *  * * ****
MAP Score: 16.8932

Motif 2
GTTTTCGTGATTATATTCACAGAAACCGGTAAG	0	56	0
ACAGAAACTTTTTTTTACTGATATCTGAAGGGT	0	135	0
ATCTGGAGGTTTCTCTACAGAAACTTTTTTTTA	0	151	0
AATTATGGCCTTTTTTACTAATATCTGGAGGTT	0	173	0
AAGGCCATAATTTTATTAAGAGGTCTTTTTTAG	0	194	1
CTAACTCACCTTTTTTAAAAAGATTTATAT   	0	229	1
ACCGGAATGATTCTATTATCATAAAC       	3	3	0
GTGCTGCTTTTTATGTTCTGTGATCATGAGGAT	5	68	1
ATAGAAAACTTTATATTATCATAAATAATCATG	7	89	1
ATTGACATAATTTTATACAGAGAAG        	8	2	0
TGATTATATATTCTGTTCTGAGGATATCTTTTA	8	121	1
          ** * **** ***
MAP Score: 10.6436

Motif 3
AGCGGTGATTATATATTCTGTTCTGAGGATATCTTTTACAGG	8	116	1
ATTTATTACTAAATCTTCTGTAGAGGGACCCTTCAGATATCA	0	108	1
    CCCCGTAAATAATCCTGAATGAGAACATGGAAGCC   	2	7	0
TGTTCTGAGAGGATCTTCAGGGGGGGGGCAGTAGCGGTGATT	8	84	1
AATGGAAGGGATTTAATCAGAAAAGAGGGGATTTA       	4	30	1
TTTAATTAATATATCATCGGGGTATTGCTGGTTTACTGATTG	5	27	1
GTTTATGATAATAGAATCATTCCGGTGTTAATGGTGATGAG 	3	10	1
TTAAGGATTTTCATAGTCGTTTTCGTGATTATATTCACAGAA	0	65	0
GATTATATTCACAGAAACCGGTAAGTGGATGTGACTCCATAG	0	39	0
TTTTCTATATAAATCGTAATAAAATAGGGGATCCGATGATTA	7	55	0
          * *** ** *    * *    *
MAP Score: 9.3058

Motif 4
ATGTGACTCCATAGGAACCTCCAGGACATGA	0	22	0
GATTATATTCACAGAAACCGGTAAGTGGATG	0	50	0
GTTTCTGTGAATATAATCACGAAAACGACTA	0	63	1
AGGTTTCTCTACAGAAACTTTTTTTTACTGA	0	147	0
AAGTTTCTGTAGAGAAACCTCCAGATATTAG	0	158	1
    CCCCGTAAATAATCCTGAATGAGAACA	2	18	0
GTTTATGATAATAGAATCATTCCGGTGTTAA	3	10	1
GTGTTTAATCATCGGATCCCCTATTTTATTA	7	50	1
ATATTATCATAAATAATCATGTTAATTATTG	7	101	1
AAGTGTTCTGAGAGGATCTTCAGGGGGGGGG	8	81	1
AGAACAGAATATATAATCACCGCTACTGCCC	8	109	0
          * *********
MAP Score: 5.45213

Motif 5
TTCCCACCCCATCATGTCCTGGAGGTTCCTATGGAGTCACAT	0	11	1
CTTTTTTTTACTGATATCTGAAGGGTCCCTCTACAGAAGATT	0	119	0
AAAAAAGGCCATAATTTTATTAAGAGGTCTTTTTTAGGTCTA	0	190	1
GTCTAACTCACCTTTTTTAAAAAGATTTATAT          	0	227	1
   GGCTTCCATGTTCTCATTCAGGATTATTTACGGGG    	2	7	1
TAAATCCCTTCCATTTTCATTCCACATCATGTCTT       	4	3	0
CATCGGATCCCCTATTTTATTACGATTTATATAGAAAACTTT	7	59	1
AGAAAACTTTATATTATCATAAATAATCATGTTAATTATTGG	7	91	1
TCTGTATAAAATTATGTCAATGGGTTACATTTAATGCTTTGC	8	14	1
GTGATTATATATTCTGTTCTGAGGATATCTTTTACAGGAGGA	8	120	1
          **  * **     *   *** *
MAP Score: 5.03614

Motif 6
CATGTCCTGGAGGTTCCTATGGAGTCACATCCAC	0	23	1
TTTATTACTAAATCTTCTGTAGAGGGACCCTTCA	0	109	1
ACTTTTTTTTACTGATATCTGAAGGGTCCCTCTA	0	128	0
CAGTAAAAAAAAGTTTCTGTAGAGAAACCTCCAG	0	148	1
GGCCTTTTTTACTAATATCTGGAGGTTTCTCTAC	0	166	0
AAAAGGCCATAATTTTATTAAGAGGTCTTTTTTA	0	192	1
GTTCTCATTCAGGATTATTTACGGGG        	2	19	1
ATGATGTGGAATGAAAATGGAAGGGATTTAATCA	4	15	1
ATGATTATTTATGATAATATAAAGTTTTCTATAT	7	87	0
ATGTTAATTATTGGTACTAAAGAGAAGGGAGCTA	7	119	1
CCATTGACATAATTTTATACAGAGAAG       	8	3	0
CTTTCTTTGAAGTGTTCTGAGAGGATCTTCAGGG	8	72	1
          * * ****  ****
MAP Score: 3.64946